1. Import cleaned .csv file and look at dataframe.

2. Remove excess columns and calcuate other factors of interest.

3. Where are the processed cores from?






4. Plotting by site and region


Below, the depth profile for organic matter (right) and inorganic mater (left) from each site is roughly plotted to compare the overall matter content. You will notice that site L06 is way different than the rest.




The core from L06 was loaded with chunky woody debris; in general, this site had a lot of woody debris at the surface of the sediment (see notes). The data are real but an outlier compared to the other sites. Here are two images of the sliced core from site L06:


For the sake of looking at regional patterns, I’ve removed Site L06 for further analysis.









Here the data are plotted again but grouped by sea otter region. In plots on the right, the sites are color coded to demonstrate the variance across sites (and in which sites); the mean values + standard error are shown on the left. The red lines represent the mean values for the entire length of the respective core.


Organic matter




Inorganic matter




OM:IM ratio










Looking at the means, it appears that OM and IM decrease as sea otters become more abundant in a region. The distribution across sites, however, looks bimodal (particularly for the Low region). Let’s look at their distributions using density plots:























For proper analysis, we need to decide how to deal with the bimodal distributions.









4. Other things? Plotting general patterns of mean core matter versus factors



Matter content * sea otter duration

I do have a question about the duration factor…there are only two year groups, 7 and 14. I don’t understand why the low sites are grouped in the 7-yr bin because some/most of those sites haven’t had sea otters at all; I would have expected a third “0-yr” category. I know that these spatial data are derived from elsewhere, but…







Matter content * sea otter index

I wouldn’t expect the buried OM and IM would interact with the sea otter index; burial relects a long/big temporal scale, where the sea otter index incorporates short-term data (e.g. cracked shells, pits).










5. Top 15 cm: might sediment type help explain OM and IM content?


A. This section only includes the top 15 cm of each core. This was decided because our qualitative assessment of sediment type at the surface is unlikely to be accurate for deeper sediment profiles. B. This section also takes the bimodal data into account; I exclude the upper clusters (Sites L01, L05, L06, M08, H06), which were identified by comparing the curves of the density plots to the sites that were plotted higher than the mean core matter. Treating each modal cluster as independent is one way to further explore patterns in the data.